The cDNA sequence of the gene for human apolipoprotein C-II and it's localization to chromosome 19 has been previously established. In addition, the complete genomic sequence of normal human apoC-II has been elucidated from an apoC-II clone isolated from a human placental genomic DNA phage library. It consists of 3407 base pairs and like the genomic structure of other known apolipoprotein genes, it contains 3 introns and 4 exons. The apoC-II gene from one patient with apoC-II deficiency has been cloned into an EMBL-3 lambda genomic library. Determination of the complete genomic structure of this patient is underway to determine the specific molecular defect in apoC-II in this kindred. Total RNA from the liver of a second patient with apoC-II deficiency has been isolated. Slot blot analysis reveal decreased levels of the apoC-II message in this patient. Analysis of the various normal apoC-II isoforms in plasma have been performed by utilizing the techniques of 2- dimensional gel electrophoresis and immunoblotting. ApoC-II consists of 4 major plasma isoforms that result from the post-translational processing of apoC-II in the form of glycosylation, deglycosylation and proteolytic cleavage. Confirmation that apoC-II is initially synthesized as a preproprotein has been obtained by amino acid composition and amino terminal sequence analysis. Similar 2-D gel studies of the plasma of 4 independent patients with apoC-II deficiency reveal 4 different abnormalities. These include: total absence of apoC-II, low levels of apoC-II with normal electrophoretic mobility, and low levels of apoC-II variants that exhibit abnormal electrophoretic mobility.